X-ray tomography, a non-destructive technique, provides three-dimensional data with a spatial resolution down to the
nanometer scale. Therefore, academia and industry as well as patients equally benefit from improvements in preparative
work, data acquisition and analysis. Since 1997, the conference on Developments in X-ray Tomography has set the
benchmark in dissemination of knowledge related to dedicated instrumentation, developments in software for
reconstruction, artefact removal and data analysis as well as to the wide range of applications. The paper summarizes
some aspects analyzing the previous volumes and the contributions in the current volume.

Retrospective gating on animal studies with microCT has gained popularity in recent years. Previously, we use ECG signals for cardiac gating and breathing airflow or video signals of abdominal motion for respiratory gating. This method is adequate and works well for most applications. However, through the years, researchers have noticed some pitfalls in the method. For example, the additional signal acquisition step may increase failure rate in practice. X-Ray image-based gating, on the other hand, does not require any extra step in the scanning. Therefore we investigate imagebased gating techniques. This paper presents a comparison study of the image-based versus signal-based approach to retrospective gating. The two application areas we have studied are respiratory and cardiac imaging for both rats and mice. Image-based respiratory gating on microCT is relatively straightforward and has been done by several other researchers and groups. This method retrieves an intensity curve of a region of interest (ROI) placed in the lung area on all projections. From scans on our systems based on step-and-shoot scanning mode, we confirm that this method is very effective. A detailed comparison between image-based and signal-based gating methods is given. For cardiac gating, breathing motion is not negligible and has to be dealt with. Another difficulty in cardiac gating is the relatively smaller amplitude of cardiac movements comparing to the respirational movements, and the higher heart rate. Higher heart rate requires high speed image acquisition. We have been working on our systems to improve the acquisition speed. A dual gating technique has been developed to achieve adequate cardiac imaging.

X-rays and neutrons provide complementary non-destructive probes for the analysis of structure and chemical
composition of materials. Contrast differences between the modes arise due to the differences in interaction with matter.
Due to the high sensitivity to hydrogen, neutrons excel at separating liquid water or hydrogenous phases from the
underlying structure while X-rays resolve the solid structure. Many samples of interest, such as fluid flow in porous
materials or curing concrete, are stochastic or slowly changing with time which makes analysis of sequential imaging
with X-rays and neutrons difficult as the sample may change between scans. To alleviate this issue, NIST has developed
a system for simultaneous X-ray and neutron tomography by orienting a 90 keVpeak micro-focus X-ray tube orthogonally
to a thermal neutron beam. This system allows for non-destructive, multimodal tomography of dynamic or stochastic
samples while penetrating through sample environment equipment such as pressure and flow vessels. Current efforts are
underway to develop methods for 2D histogram based segmentation of reconstructed volumes. By leveraging the
contrast differences between X-rays and neutrons, greater histogram peak separation can occur in 2D vs 1D enabling
improved material identification.

In this work we present x-ray phase-contrast tomography of heart tissue from mouse, combining computed tomography (CT) scans with laboratory and synchrotron radiation. The work serves as a proof-of-concept that the cyto-architecture and in particular the myofibril orientation can be assessed in three dimensions (3D) by phase-contrast CT. We demonstrate the synergistic use of laboratory μ-CT and of the high resolution synchrotron setup based on waveguide optics. Details on preparation, instrumentation and analysis are given, as a state of the art reference for heart tissue tomography, and as a starting point for further progress.

In high-resolution tomography, one needs high-resolved projections in order to reconstruct a high-quality 3D map of a sample. X-ray ptychography is a robust technique which can provide such high-resolution 2D projections taking advantage of coherent X-rays. This technique was used in the far-field regime for a fair amount of time, but it can now also be implemented in the near-field regime. In both regimes, the technique enables not only high-resolution imaging, but also high sensitivity to the electron density of the sample. The combination with tomography makes 3D imaging possible via ptychographic X-ray computed tomography (PXCT), which can provide a 3D map of the complex-valued refractive index of the sample. The extension of PXCT to X-ray energies above 15 keV is challenging, but it can allow the imaging of object opaque to lower energy. We present here the implementation and developments of high-energy near- and far-field PXCT at the ESRF.

The implementation of X-Ray Phase Contrast (XPC) imaging at synchrotrons has demonstrated transformative potential on a wide range of applications, from medicine and biology to materials science. However, translation to conventional laboratory sources has proven more problematic, because of XPC’s stringent requirements in terms of spatial coherence. This has imposed the use of either micro-focal sources, or collimators (e.g. source gratings) where sources with extended focal spots were used. This reduces the available x-ray flux leading to long exposure times, which is often exacerbated by the use of additional optical elements that need to be scanned during image acquisition. Where these elements are placed downstream of the object, they also lead to an increase in the delivered dose.
XPC has also been successfully adapted to full 3D, computed tomography (CT) implementations, which has however exacerbated the above concerns in terms of acquisition times and delivered doses.
We tackled this problem by developing an incoherent approach to XPC that works with non micro-focal laboratory sources without requiring any additional collimation. The method uses one or two low aspect ratio x-ray masks that are built on low-absorbing graphite substrates for maximum transmission through the mask apertures. The combination of this with a “single-shot” phase retrieval algorithm has enabled the development of a lab-based XPC-CT system that can perform a full scan in a few minutes while delivering low radiation doses. The talk will briefly describe how the method works, then show application examples including direct comparisons with the synchrotron gold standard.

Phase-contrast imaging has proven to be a valuable tool when investigating weak absorbing materials like soft tissue, due to its increased contrast compared to conventional absorption-contrast imaging. While propagation-based phase-contrast is an ideal tool to achieve highest resolution at a good contrast for almost not-absorbing material, it quickly comes to its limitations on applications demanding for a high dynamic range in contrast. For those applications grating-based phase-contrast is the tool of choice, although it lacks of spatial resolution compared to inline phase-contrast or attenuation-based microCT. To reduce this gap in spatial resolution we equipped the two PETRA III beamlines P05 and P07 with a customized set of mechanics to maximize the performance of the interferometer. After latest optimization steps our system allows for phase-contrast measurements in a continuous energy range between 10 keV and 80 keV . Dependent on investigated material and energy the setup is capable to achieve a spatial resolution of 5 μm on a field of view of 6.5 mm. We will present our implementation of grating-based phase-contrast computed tomography for fast and high-resolution measurements at the PETRA III along with its recent optimization, and demonstrate its performance based on different kinds of applications.

Grating-based X-ray phase contrast and scattering contrast tomography were pioneered at synchrotron beamlines and are well established as laboratory applications. The interpretation and appropriate signal reconstruction of scattering contrast (so called dark-field image contrast DIC) long remained an issue vividly discussed in the scientific community. Based on its interpretation as ultra-small angle scattering by microscopic interfaces (e.g., fibers, pores or particles) we present examples from various micro-structured materials imaged with our specific setup equipped with a liquid metal jet X-ray source and a high and medium resolution detector. Besides DIC, grating based phase contrast further provides the complementary contrast modes of attenuation and differential phase contrast. From these two contrasts, a comparison of propagation based phase contrast (in-line phase contrast) and differential phase contrast will be shown.

X-ray diffraction can be used as the signal for tomographic reconstruction and provides a cross-sectional map of the
crystallographic phases and related quantities. Diffraction tomography has been developed over the last decade using
monochromatic x-radiation and an area detector. This paper reports tomographic reconstruction with polychromatic
radiation and an energy sensitive detector array. The energy dispersive diffraction (EDD) geometry, the instrumentation
and the reconstruction process are described and related to the expected resolution. Results of EDD tomography are
presented for two samples containing hydroxyapatite (hAp). The first is a 3D-printed sample with an elliptical crosssection
and contains synthetic hAp. The second is a human second metacarpal bone from the Roman-era cemetery at
Ancaster, UK and contains bio-hAp which may have been altered by diagenesis. Reconstructions with different
diffraction peaks are compared. Prospects for future EDD tomography are also discussed.

Communication among humans occurs through coding and decoding of acoustic information. The inner ear or cochlea acts as a frequency analyzer and divides the acoustic signal into small frequency bands, which are processed at different sites along the cochlea. The mechano-electrical conversion is accomplished by the soft tissue structures in the cochlea. While the anatomy for most of the cochlea has been well described, a detailed description of the very high frequency and vulnerable cochlear hook region is missing. To study the cochlear hook, mice cochleae were imaged with synchrotron radiation and high-resolution reconstructions have been made from the tomographic scans. This is the first detailed description of the bony and soft tissues of the hook region of the mammalian cochlea.

Talbot interferometer using white synchrotron radiation has been demonstrated for time-resolved X-ray phase imaging and tomography as well as four-dimensional phase tomography to observe dynamics in samples. In this study, X-ray phase tomography has been used to follow the time evolution of phase separation in polymer blend through heating treatment. For this purpose, we performed in-situ X-ray phase imaging and tomography with X-ray Talbot-Lau interferometer using white synchrotron radiation. The X-ray Talbot-Lau interferometer consisted of a source grating (30 μm in period), a π/2 phase grating (4.5 μm in period), an amplitude grating (5.3 μm in period) and a high-speed camera. A polymer blend sample of polystyrene (PS) (Mw = 76,500) and polymethyl methacrylate (PMMA) (Mw = 33,200) was used for the CT observation. A compound of the PS and PMMA was made by a twin-screw kneading extruder and put into an Al tube whose inner diameter was 6 mm. The sample temperature was maintained at desired temperature sequence by controlling a lamp for heating, and CT scans were repeated to track the changes in sample structures at a temporal resolution of 5 seconds. PS-rich phase and PMMA-rich phase changing with time evolution were revealed.

Multi-modality imaging methods are instrumental for advanced diagnosis and therapy. Specifically, a hybrid system that combines computed tomography (CT), nuclear imaging, and magnetic resonance imaging (MRI) will be a Holy Grail of medical imaging, delivering complementary structural/morphological, functional, and molecular information for precision medicine. A novel imaging method was recently demonstrated that takes advantage of radiotracer polarization to combine MRI principles with nuclear imaging. This approach allows the concentration of a polarized Υ-ray emitting radioisotope to be imaged with MRI resolution potentially outperforming the standard nuclear imaging mode at a sensitivity significantly higher than that of MRI. In our work, we propose to acquire MRI-modulated nuclear data for simultaneous image reconstruction of both emission and transmission parameters, suggesting the potential for simultaneous CT-SPECT-MRI. The synchronized diverse datasets allow excellent spatiotemporal registration and unique insight into physiological and pathological features. Here we describe the methodology involving the system design with emphasis on the formulation for tomographic images, even when significant radiotracer signals are limited to a region of interest (ROI). Initial numerical results demonstrate the feasibility of our approach for reconstructing concentration and attenuation images through a head phantom with various radio-labeled ROIs. Additional considerations regarding the radioisotope characteristics are also discussed.

In spectral CT, an energy-resolving detector is capable of counting the number of received photons in different energy channels with appropriate post-processing steps. Because the received photon number in each energy channel is low in practice, the generated projections suffer from low signal-to-noise ratio. This poses a challenge to perform image reconstruction of spectral CT. Because the reconstructed multi-channel images are for the same object but in different energies, there is a high correlation among these images and one can make full use of this redundant information. In this work, we propose a weighted block-matching and three-dimensional (3-D) filtering (BM3D) based method for spectral CT denoising. It is based on denoising of small 3-D data arrays formed by grouping similar 2-D blocks from the whole 3-D data image. This method consists of the following two steps. First, a 2-D image is obtained using the filtered back-projection (FBP) in each energy channel. Second, the proposed weighted BM3D filtering is performed. It not only uses the spatial correlation within each channel image but also exploits the spectral correlation among the channel images. The proposed method is evaluated on both numerical simulation and realistic preclinical datasets, and its merits are demonstrated by the promising results.

X-ray phase CT has a potential to give the higher contrast in soft tissue observations. To shorten the measure- ment time, sparse-view CT data acquisition has been attracting the attention. This paper applies two major compressed sensing (CS) approaches to image reconstruction in the x-ray sparse-view phase tomography. The first CS approach is the standard Total Variation (TV) regularization. The major drawbacks of TV regularization are a patchy artifact and loss in smooth intensity changes due to the piecewise constant nature of image model. The second CS method is a relatively new approach of CS which uses a nonlinear smoothing filter to design the regularization term. The nonlinear filter based CS is expected to reduce the major artifact in the TV regular- ization. The both cost functions can be minimized by the very fast iterative reconstruction method. However, in the past research activities, it is not clearly demonstrated how much image quality diﬀerence occurs between the TV regularization and the nonlinear filter based CS in x-ray phase CT applications. We clarify the issue by applying the two CS applications to the case of x-ray phase tomography. We provide results with numerically simulated data, which demonstrates that the nonlinear filter based CS outperforms the TV regularization in terms of textures and smooth intensity changes.

Given the potential risk of X-ray radiation to the patient, low-dose CT has attracted a considerable interest in the medical imaging field. Currently, the main stream low-dose CT methods include vendor-specific sinogram domain filtration and iterative reconstruction algorithms, but they need to access raw data whose formats are not transparent to most users. Due to the difficulty of modeling the statistical characteristics in the image domain, the existing methods for directly processing reconstructed images cannot eliminate image noise very well while keeping structural details. Inspired by the idea of deep learning, here we combine the autoencoder, deconvolution network, and shortcut connections into the residual encoder-decoder convolutional neural network (RED-CNN) for low-dose CT imaging. After patch-based training, the proposed RED-CNN achieves a competitive performance relative to the-state-of-art methods. Especially, our method has been favorably evaluated in terms of noise suppression and structural preservation.

Machine learning has revolutionized a number of fields, but many micro-tomography users have never used it for their work. The micro-tomography beamline at the Advanced Light Source (ALS), in collaboration with the Center for Applied Mathematics for Energy Research Applications (CAMERA) at Lawrence Berkeley National Laboratory, has now deployed a series of tools to automate data processing for ALS users using machine learning. This includes new reconstruction algorithms, feature extraction tools, and image classification and recommen- dation systems for scientific image. Some of these tools are either in automated pipelines that operate on data as it is collected or as stand-alone software. Others are deployed on computing resources at Berkeley Lab–from workstations to supercomputers–and made accessible to users through either scripting or easy-to-use graphical interfaces. This paper presents a progress report on this work.

Brain tissues have been an attractive subject for investigations in neuropathology, neuroscience, and neurobiol- ogy. Nevertheless, existing imaging methodologies have intrinsic limitations in three-dimensional (3D) label-free visualisation of extended tissue samples down to (sub)cellular level. For a long time, these morphological features were visualised by electron or light microscopies. In addition to being time-consuming, microscopic investigation includes specimen fixation, embedding, sectioning, staining, and imaging with the associated artefacts. More- over, optical microscopy remains hampered by a fundamental limit in the spatial resolution that is imposed by the diffraction of visible light wavefront. In contrast, various tomography approaches do not require a complex specimen preparation and can now reach a true (sub)cellular resolution. Even laboratory-based micro computed tomography in the absorption-contrast mode of formalin-fixed paraffin-embedded (FFPE) human cerebellum yields an image contrast comparable to conventional histological sections. Data of a superior image quality was obtained by means of synchrotron radiation-based single-distance X-ray phase-contrast tomography enabling the visualisation of non-stained Purkinje cells down to the subcellular level and automated cell counting. The question arises, whether the data quality of the hard X-ray tomography can be superior to optical microscopy. Herein, we discuss the label-free investigation of the human brain ultramorphology be means of synchrotron radiation-based hard X-ray magnified phase-contrast in-line tomography at the nano-imaging beamline ID16A (ESRF, Grenoble, France). As an example, we present images of FFPE human cerebellum block. Hard X-ray tomography can provide detailed information on human tissues in health and disease with a spatial resolution below the optical limit, improving understanding of the neuro-degenerative diseases.

Bone properties at all length scales have a major impact on the fracture risk in disease such as osteoporosis. However, quantitative 3D data on bone tissue at the cellular scale are still rare. Here we propose to use magnified X-ray phase nano-CT to quantify bone ultra-structure in human bone, on the new setup developed on the beamline ID16A at the ESRF, Grenoble. Obtaining 3D images requires the application of phase retrieval prior to tomographic reconstruction. Phase retrieval is an ill-posed problem for which various approaches have been developed. Since image quality has a strong impact on the further quantification of bone tissue, our aim here is to evaluate different phase retrieval methods for imaging bone samples at the cellular scale. Samples from femurs of female donors were scanned using magnified phase nano-CT at voxel sizes of 120 and 30 nm with an energy of 33 keV. Four CT scans at varying sample-to-detector distances were acquired for each sample. We evaluated three phase retrieval methods adapted to these conditions: Paganin’s method at single distance, Paganin’s method extended to multiple distances, and the contrast transfer function (CTF) approach for pure phase objects. These methods were used as initialization to an iterative refinement step. Our results based on visual and quantitative assessment show that the use of several distances (as opposed to single one) clearly improves image quality and the two multi-distance phase retrieval methods give similar results. First results on the segmentation of osteocyte lacunae and canaliculi from such images are presented.

To achieve the 2°C target made in the 2016 Paris Agreement, it is essential to reduce the emission of CO2 into the atmosphere. Carbon Capture and Storage (CCS) has been given increasing importance over the last decade. One of the suggested methods for CCS is to inject CO2 into geologic settings such as the carbonate reservoirs in the North Sea. The final aim of our project is to find out how to control the evolution of petrophysical parameters during CO2 injection using an optimal combination of flow rate, injection pressure and chemical composition of the influent. The first step to achieve this is to find a suitable condition to create a stable 3D space in carbonate rock by injecting liquid to prepare space for the later CO2 injection. Micro-CT imaging is a non-destructive 3D method that can be used to study the property changes of carbonate rocks during and after CO2 injection. The advance in lab source based micro-CT has made it capable of in situ experiments. We used a commercial bench top micro-CT (Zeiss Versa XRM410) to study the microstructure changes of chalk during liquid injection. Flexible temporal CT resolution is essential in this study because that the time scales of coupled physical and chemical processes can be very different. The results validated the feasibility of using a bench top CT system with a pressure cell to monitor the mesoscale multiphase interactions in chalk.

Internal porosity is an inherent phenomenon to many manufacturing processes, such as casting, additive manufacturing, and others. Since these defects cannot be completely avoided by improving production processes, it is important to have a reliable method to detect and evaluate them accurately. The accurate evaluation becomes even more important concerning current industrial trends to minimize size and weight of products on one side, and enhance their complexity and performance on the other. X-ray computed tomography (CT) has emerged as a promising instrument for holistic porosity measurements offering several advantages over equivalent methods already established in the detection of internal defects. The main shortcomings of the conventional techniques pertain to too general information about total porosity content (e.g. Archimedes method) or the destructive way of testing (e.g. microscopy of cross-sections). On the contrary, CT is a nondestructive technique providing complete information about size, shape and distribution of internal porosity. However, due to the lack of international standards and the fact that it is relatively a new measurement technique, CT as a measurement technology has not yet reached maturity. This study proposes a procedure for the establishment of measurement traceability in porosity measurements by CT including the necessary evaluation of measurement uncertainty. The traceability transfer is carried out through a novel reference standard calibrated by optical and tactile coordinate measuring systems. The measurement uncertainty is calculated following international standards and guidelines. In addition, the accuracy of porosity measurements by CT with the associated measurement uncertainty is evaluated using the reference standard.

Permanent implants made of titanium or its alloys are the gold standard in many orthopedic and traumatological
applications due to their good biocompatibility and mechanical properties. However, a second surgical intervention is
required for this kind of implants as they have to be removed in the case of children that are still growing or on patient’s
demand. Therefore, magnesium-based implants are considered for medical applications as they are degraded under
physiological conditions. The major challenge is tailoring the degradation in a manner that is suitable for a biological
environment and such that stabilization of the bone is provided for a controlled period. In order to understand failure
mechanisms of magnesium-based implants in orthopedic applications and, further, to better understand the
osseointegration, screw implants in bone are studied under mechanical load by means of a push-out device installed at
the imaging beamline P05 of PETRA III at DESY. Conventional absorption contrast microtomography and phasecontrast
techniques are applied in order to monitor the bone-to-implant interface under increasing load conditions. In this
proof-of-concept study, first results from an in situ push-out experiment are presented.

Beamtime and resulting SRμCT data are a valuable resource for researchers of a broad scientific community in life sciences. Most research groups, however, are only interested in a specific organ and use only a fraction of their data. The rest of the data usually remains untapped. By using a new collaborative approach, the NOVA project (Network for Online Visualization and synergistic Analysis of tomographic data) aims to demonstrate, that more efficient use of the valuable beam time is possible by coordinated research on different organ systems. The biological partners in the project cover different scientific aspects and thus serve as model community for the collaborative approach. As proof of principle, different aspects of insect head morphology will be investigated (e.g., biomechanics of the mouthparts, and neurobiology with the topology of sensory areas). This effort is accomplished by development of advanced analysis tools for the ever-increasing quantity of tomographic datasets. In the preceding project ASTOR, we already successfully demonstrated considerable progress in semi-automatic segmentation and classification of internal structures. Further improvement of these methods is essential for an efficient use of beam time and will be refined in the current NOVAproject. Significant enhancements are also planned at PETRA III beamline p05 to provide all possible contrast modalities in x-ray imaging optimized to biological samples, on the reconstruction algorithms, and the tools for subsequent analyses and management of the data. All improvements made on key technologies within this project will in the long-term be equally beneficial for all users of tomography instrumentations.

Energy resolved detectors are gaining traction as a tool to achieve better material contrast. K-edge imaging and tomography is an example of a method with high potential that has evolved on the capabilities of photon counting energy dispersive detectors. Border security is also beginning to see instruments taking advantage of energy resolved detectors. The progress of the field is halted by the limitations of the detectors. The limitations include nonlinear response for both x-ray intensity and x-ray spectrum. In this work we investigate how the physical interactions in the energy dispersive detectors affect the quality of the reconstruction and how corrections restore the quality. We have modeled detector responses for the primary detrimental effects occurring in the detector; escape peaks, charge sharing/loss and pileup. The effect of the change in the measured spectra is evaluated based on the artefacts occurring in the reconstructed images. We also evaluate the effect of a correction algorithm for reducing these artefacts on experimental data acquired with a setup using Multix ME-100 V-2 line detector modules. The artefacts were seen to introduce 20% deviation in the reconstructed attenuation coefficient for the uncorrected detector. We performed tomography experiments on samples with various materials interesting for security applications and found the SSIM to increase >; 5% below 60keV. Our work shows that effective corrections schemes are necessary for the accurate material classification in security application promised by the advent of high flux detectors for spectral tomography

The phase-stepping (PS) mode of X-ray Grating Talbot interferometer (XGTI) data processing technique can yield
high-spatial resolution images, albeit with lower throughput since each projection of a tomogram requires at least five
phase-stepping images. To overcome this problem, we can use a setup with only a single phase grating in combination
with a high-resolution detector system and a Spatial Harmonic Imaging (SHI) technique. The latter technique makes use
of the fact that a Talbot interferogram consists of carrier frequency spectrum of the grating overlapping with the sample
spectrum and by Fourier transforming the interferogram we can separate the two. The disadvantage of this is that the
spatial resolution is inferior. In this manuscript we will compare these two single grating data processing techniques
using a single data set measured with mouse embryo heart and discuss advantages and disadvantages of each technique.
These two techniques can be used as complementary; one for high resolution, and the other for high-speed imaging.

The Diamond Beamline I13L is dedicated to imaging on the micro- and nano-lengthsale, operating in the energy range
between 6 and 30keV. For this purpose two independently operating branchlines and endstations have been built. The
imaging branch is fully operational for micro-tomography and in-line phase contrast imaging with micrometre
resolution. Grating interferometry is currently implemented, adding the capability of measuring phase and small-angle
information. For tomography with increased resolution a full-field microscope providing 50nm spatial resolution with a
field of view of 100μm is being tested. The instrument provides a large working distance between optics and sample to
adapt a wide range of customised sample environments. On the coherence branch coherent diffraction imaging
techniques such as ptychography, coherent X-ray diffraction (CXRD) are currently developed for three dimensional
imaging with the highest resolution.
The imaging branch is operated in collaboration with Manchester University, called therefore the Diamond-Manchester
Branchline. The scientific applications cover a large area including bio-medicine, materials science, chemistry geology
and more. The present paper provides an overview about the current status of the beamline and the science addressed.

4D X-ray computed tomography (4D-XCT) is widely used to perform non-destructive characterization of time varying physical processes in various materials. The conventional approach to improving temporal resolution in 4D-XCT involves the development of expensive and complex instrumentation that acquire data faster with reduced noise. It is customary to acquire data with many tomographic views at a high signal to noise ratio. Instead, temporal resolution can be improved using regularized iterative algorithms that are less sensitive to noise and limited views. These algorithms benefit from optimization of other parameters such as the view sampling strategy while improving temporal resolution by reducing the total number of views or the detector exposure time. This paper presents the design principles of 4D-XCT experiments when using regularized iterative algorithms derived using the framework of model-based reconstruction. A strategy for performing 4D-XCT experiments is presented that allows for improving the temporal resolution by progressively reducing the number of views or the detector exposure time. Theoretical analysis of the effect of the data acquisition parameters on the detector signal to noise ratio, spatial reconstruction resolution, and temporal reconstruction resolution is also presented in this paper.

Patients usually contain various metallic implants (e.g. dental fillings, prostheses), causing severe artifacts in the x-ray CT images. Although a large number of metal artifact reduction (MAR) methods have been proposed in the past four decades, MAR is still one of the major problems in clinical x-ray CT. In this work, we develop a convolutional neural network (CNN) based MAR framework, which combines the information from the original and corrected images to suppress artifacts. Before the MAR, we generate a group of data and train a CNN. First, we numerically simulate various metal artifacts cases and build a dataset, which includes metal-free images (used as references), metal-inserted images and various MAR methods corrected images. Then, ten thousands patches are extracted from the databased to train the metal artifact reduction CNN. In the MAR stage, the original image and two corrected images are stacked as a three-channel input image for CNN, and a CNN image is generated with less artifacts. The water equivalent regions in the CNN image are set to a uniform value to yield a CNN prior, whose forward projections are used to replace the metal affected projections, followed by the FBP reconstruction. Experimental results demonstrate the superior metal artifact reduction capability of the proposed method to its competitors.

Artifacts resulting from metal objects have been a persistent problem in CT images over the last four decades. A common
approach to overcome their effects is to replace corrupt projection data with values synthesized from an interpolation
scheme or by reprojection of a prior image. State-of-the-art correction methods, such as the interpolation- and
normalization-based algorithm NMAR, often do not produce clinically satisfactory results. Residual image artifacts remain
in challenging cases and even new artifacts can be introduced by the interpolation scheme. Metal artifacts continue to be
a major impediment, particularly in radiation and proton therapy planning as well as orthopedic imaging. A new solution
to the long-standing metal artifact reduction (MAR) problem is deep learning, which has been successfully applied to
medical image processing and analysis tasks. In this study, we combine a convolutional neural network (CNN) with the
state-of-the-art NMAR algorithm to reduce metal streaks in critical image regions. Training data was synthesized from CT
simulation scans of a phantom derived from real patient images. The CNN is able to map metal-corrupted images to
artifact-free monoenergetic images to achieve additional correction on top of NMAR for improved image quality. Our
results indicate that deep learning is a novel tool to address CT reconstruction challenges, and may enable more accurate
tumor volume estimation for radiation therapy planning.

This paper review the configurations of grating-based X-ray interferometry for X-ray phase imaging/tomography and describes recent activities for four-dimensional X-ray phase tomography and nanoscopic X-ray phase tomog-
raphy. A multilayer mirror to produce a 10% bandwidth pink beam at 25 keV has been installed at SPring-8 for four-dimensional X-ray phase tomography, and an application to polymer laser ablation is presented. A 100-fold full-field X-ray microscope employing a Fresnel zone plate has been used successfully in combination with a Talbot interferometer to perform nanoscopic phase tomography for a malleal processus brevis of a mouse nine days after birth. Another development using a laboratory-based full-field X-ray microscope in combination with a Lau interferometer is also described.

Based on the collision of intense laser and relativistic electrons, a Thomson scattering x-ray source can produce quasi-monochromatic x-ray pulses with high brightness in the tens keV or even higher energy regime, which can eliminate the beam hardening effect encountered in computed tomography (CT) by using polychromatic x-rays generated through Bremsstrahlung and make it possible to relate the reconstructed linear attenuation coefficients to the composition of a material. In this paper, we demonstrate the capacity of quantitative CT measurement based on Tsinghua Thomson scattering X-ray source (TTX) and the potential of anatomical segmentation using quantitative linear attenuation coefficient analysis. A peanut sample (Arachis hypogaea L.) was chosen for this study. According to the reconstructed CT image, all anatomical structures except for the testa (i.e. the seed coat) of peanut were identified clearly in terms of the shape and size, and there were high similarities between reconstructed linear attenuation coefficients of cotyledon and its theoretical values. After quantitative analysis of the reconstructed linear attenuation coefficients, the hull can be peeled off the core at the threshold of 0.31 cm-1. Our results pave the way towards fundamental researches and practical applications based on quantitative CT at TTX.

An X-ray phase tomographic microscope that can quantitatively measure the refractive index of a sample in three dimensions with a high spatial resolution was developed by installing a Lau interferometer consisting of an absorption grating and a π/2 phase grating into the optics of an X-ray microscope. The optics comprises a Cu rotating anode X-ray source, capillary condenser optics, and a Fresnel zone plate for the objective. The microscope has two optical modes: a large-field-of-view mode (field of view: 65 μm x 65 μm) and a high-resolution mode (spatial resolution: 50 nm). Optimizing the parameters of the interferometer yields a self-image of the phase grating with ~60% visibility. Through the normal fringe-scanning measurement, a twin phase image, which has an overlap of two phase image of opposite contrast with a shear distance much larger than system resolution, is generated. Although artifacts remain to some extent currently when a phase image is calculated from the twin phase image, this system can obtain high-spatial-resolution images resolving 50-nm structures. Phase tomography with this system has also been demonstrated using a phase object.

Recent progress in X-ray CT is contributing to the advent of new clinical applications. A common challenge for these applications is the need for new image reconstruction methods that meet tight constraints in radiation dose and geometrical limitations in the acquisition. The recent developments in sparse reconstruction methods provide a framework that permits obtaining good quality images from drastically reduced signal-to-noise-ratio and limited-view data. In this work, we present our contributions in this field. For dynamic studies (3D+Time), we explored the possibility of extending the exploitation of sparsity to the temporal dimension: a temporal operator based on modelling motion between consecutive temporal points in gated-CT and based on experimental time curves in contrast-enhanced CT. In these cases, we also exploited sparsity by using a prior image estimated from the complete acquired dataset and assessed the effect on image quality of using different sparsity operators. For limited-view CT, we evaluated total-variation regularization in different simulated limited-data scenarios from a real small animal acquisition with a cone-beam microCT scanner, considering different angular span and number of projections. For other emerging imaging modalities, such as spectral CT, the image reconstruction problem is nonlinear, so we explored new efficient approaches to exploit sparsity for multi-energy CT data. In conclusion, we review our approaches to challenging CT data reconstruction problems and show results that support the feasibility for new clinical applications.

Recent developments in multispectral X-ray detectors allow for an efficient identification of materials based on their chemical composition. This has a range of applications including security inspection, which is our motivation. In this paper, we analyze data from a tomographic setup employing the MultiX detector, that records projection data in 128 energy bins covering the range from 20 to 160 keV. Obtaining all information from this data requires reconstructing 128 tomograms, which is computationally expensive. Instead, we propose to reduce the dimensionality of projection data prior to reconstruction and reconstruct from the reduced data. We analyze three linear methods for dimensionality reduction using a dataset with 37 equally-spaced projection angles. Four bottles with different materials are recorded for which we are able to obtain similar discrimination of their content using a very reduced subset of tomograms compared to the 128 tomograms that would otherwise be needed without dimensionality reduction.

In hard X-ray microtomography, ring artefacts regularly originate from incorrectly functioning pixel elements on the detector or from particles and scratches on the scintillator. We show that due to the high sensitivity of contemporary beamline setups further causes inducing inhomogeneities in the impinging wavefronts have to be considered. We propose in this study a method to correct the thereby induced failure of simple flatfield approaches. The main steps of the pipeline are (i) registration of the reference images with the radiographs (projections), (ii) integration of the flat-field corrected projection over the acquisition angle, (iii) high-pass filtering of the integrated projection, (iv) subtraction of filtered data from the flat-field corrected projections. The performance of the protocol is tested on data sets acquired at the beamline ID19 at ESRF using single distance phase tomography.

X-ray phase contrast imaging is attracting more and more interest. Since the phase cannot be measured directly
an indirect method using e.g. a grating interferometer has to be applied. This contribution compares three
different approaches to calculate the phase from Talbot-Lau interferometer measurements using a phase-stepping
approach. Besides the usually applied Fourier coefficient method also a linear fitting technique and Taylor series
expansion method are applied and compared.

Even the simplest problem of monochromatic scalar absorption tomography becomes non linear when the source and detectors elements are no longer treated as points. This has variously been described as non-linear partial volume effect or exponential edge effect. We show that the nonlinearity is significant in practical fast tomography systems such as the Bergen gamma tomography system used for inspection of flows in pipes. We describe an iterative reconstruction algorithm for reconstruction using this model and present numerical results. Other non- linear problems arise in rich tomography methods and as a simple example we describe the non-Ableian problem of neutron spin tomography used for imaging magnetic domains.

For the investigation of soft tissues or tissues consisting of soft and hard tissues on the microscopic level, hard X-ray phase tomography has become one of the most suitable imaging techniques. Besides other phase contrast methods grating interferometry has the advantage of higher sensitivity than inline methods and the quantitative results. One disadvantage of the conventional double-grating setup (XDGI) compared to inline methods is the limitation of the spatial resolution. This limitation can be overcome by removing the analyser grating resulting in a single-grating setup (XSGI). In order to verify the performance of XSGI concerning contrast and spatial resolution, a quantitative comparison of XSGI and XDGI tomograms of a human nerve was performed. Both techniques provide sufficient contrast to allow for the distinction of tissue types. The spatial resolution of the two-fold binned XSGI data set is improved by a factor of two in comparison to XDGI which underlies its performance in tomography of soft tissues. Another application for grating-based X-ray phase tomography is the simultaneous visualization of soft and hard tissues of a plaque-containing coronary artery. The simultaneous visualization of both tissues is important for the segmentation of the lumen. The segmented data can be used for flow simulations in order to obtain information about the three-dimensional wall shear stress distribution needed for the optimization of mechano-sensitive nanocontainers used for drug delivery.

Water transport from roots to shoots is a vital necessity in trees in order to sustain their photosynthetic activity and, hence, their physiological activity. The vascular tissue in charge is the woody body of root, stem and branches. In gymnosperm trees, like spruce trees (Picea abies (L.) Karst.), vascular tissue consists of tracheids: elongated, protoplast- free cells with a rigid cell wall that allow for axial water transport via their lumina. In order to analyze the over-all water transport capacity within one growth ring, time-consuming light microscopy analysis of the woody sample still is the conventional approach for calculating tracheid lumen area. In our investigations at the Imaging Beamline (IBL) operated by the Helmholtz-Zentrum Geesthacht (HZG) at PETRA III storage ring of the Deutsches Elektronen-Synchrotron DESY, Hamburg, we applied SRμCT on small wood samples of spruce trees in order to visualize and analyze size and formation of xylem elements and their respective lumina. The selected high-resolution phase-contrast technique makes full use of the novel 20 MPixel CMOS area detector developed within the cooperation of HZG and the Karlsruhe data by light microscopy analysis and, hence, prove, that μCT is a most appropriate method to gain valid information on xylem cell structure and tree water transport capacity.

X-ray microtomography (XMT) is a well-established technique in dental research. The technique has been used extensively to explore the complex morphology of the root canal system, and to qualitatively and quantitatively evaluate root canal instrumentation and filling efficacy in extracted teeth; enabling different techniques to be compared. Densitometric information can be used to identify and map demineralized tissue resulting from tooth decay (caries) and, in extracted teeth, the method can be used to evaluate different methods of excavation. More recently, high contrast XMT is being used to investigate the relationship between external insults to teeth and the pulpal reaction. When such insults occur, fluid may flow through dentinal tubules as a result of cracking or porosity in enamel. Over time, there is an increase in mineralization along the paths of the tubules from the pulp to the damaged region in enamel and this can be visualized using high contrast XMT. The scanner used for this employs time-delay integration to minimize the effects of detector inhomogeneity in order to greatly increase the upper limit on signal-to-noise ratio that can be achieved with long exposure times. When enamel cracks are present in extracted teeth, the presence of these pathways indicates that the cracking occurred prior to extraction. At high contrast, growth lines are occasionally seen in deciduous teeth which may have resulted from periods of maternal illness. Various other anomalies in mineralization resulting from trauma or genetic abnormalities can also be investigated using this technique.

Tooth cementum annulation (TCA) is used by anthropologists to decipher age-at-death and stress periods based on
yearly deposited incremental lines (ILs). The destructive aspect of the TCA method, which requires cutting the tooth root
in sections to display the ILs, using transmission light microscopy, can be problematic for archeological teeth, and so a
non-invasive imaging technique is preferred. The purpose of this study is to evaluate conventional micro computed
tomography (μCT) and synchrotron radiation-based X-ray micro computed tomography (SRμCT) as a non-destructive
technique to explore the tooth cementum ultrastructure and to display ILs. Seven archeological teeth from the Basel-
Spitalfriedhof collection (patients died between 1845 and 1868 in the city hospital) were selected for the μCT
experiments. This collection is considered a unique worldwide reference series in the anthropological science
community, due to the high level of documented life history data in the medical files and the additionally collected and
verified birth history by genealogists. The results demonstrate that the conventional μCT is complementary to the
SRμCT allowing to prescreen the teeth using conventional μCT to identify the appropriate specimens and areas for the
SRμCT measurements. SRμCT displayed cementum ring structure corresponding to the ILs in the microscope view in
archeological teeth in a non-invasive fashion with the potential for more accurate assessments of ILs compared to
conventional techniques. The ILs were mainly clearly visible, and it was possible to count them for age-at-death
assessment and identify qualitatively irregular ILs which could constitute stress markers.

A high energy X-ray micro-tomography system has been developed at BL20B2 in SPring-8. The available range of the
energy is between 20keV and 113keV with a Si (511) double crystal monochromator. The system enables us to image
large or heavy materials such as fossils and metals. The X-ray image detector consists of visible light conversion system
and sCMOS camera. The effective pixel size is variable by changing a tandem lens between 6.5 μm/pixel and 25.5
μm/pixel discretely. The format of the camera is 2048 pixels x 2048 pixels. As a demonstration of the system, alkaline
battery and a nodule from Bolivia were imaged. A detail of the structure of the battery and a female mold Trilobite were
successfully imaged without breaking those fossils.

While standard computed tomography (CT) data do not depend on energy, spectral computed tomography (SPCT) acquire energy-resolved data, which allows material decomposition of the object of interest. Decompo- sitions in the projection domain allow creating projection mass density (PMD) per materials. From decomposed projections, a tomographic reconstruction creates 3D material density volume. The decomposition is made pos- sible by minimizing a cost function. The variational approach is preferred since this is an ill-posed non-linear inverse problem. Moreover, noise plays a critical role when decomposing data. That is why in this paper, a new data fidelity term is used to take into account of the photonic noise. In this work two data fidelity terms were investigated: a weighted least squares (WLS) term, adapted to Gaussian noise, and the Kullback-Leibler distance (KL), adapted to Poisson noise. A regularized Gauss-Newton algorithm minimizes the cost function iteratively. Both methods decompose materials from a numerical phantom of a mouse. Soft tissues and bones are decomposed in the projection domain; then a tomographic reconstruction creates a 3D material density volume for each material. Comparing relative errors, KL is shown to outperform WLS for low photon counts, in 2D and 3D. This new method could be of particular interest when low-dose acquisitions are performed.

Recent advances in cadmium telluride (CdTe) energy-discriminating pixelated detectors have enabled the possibility of Multi-Spectral X-ray Computed Tomography (MSXCT) to incorporate spectroscopic information into CT. MultiX ME 100 V2 is a CdTe-based spectroscopic x-ray detector array capable of recording energies from 20 to 160 keV in 1.1 keV energy bin increments. Hardware and software have been designed to perform radiographic and computed tomography tasks with this spectroscopic detector. Energy calibration is examined using the end-point energy of a bremsstrahlung spectrum and radioisotope spectral lines. When measuring the spectrum from Am-241 across 500 detector elements, the standard deviation of the peak-location and FWHM measurements are ± 0.4 and ± 0.6 keV, respectively. As these values are within the energy bin size (1.1 keV), detector elements are consistent with each other. The count rate is characterized, using a nonparalyzable model with a dead time of 64 ± 5 ns. This is consistent with the manufacturer’s quoted per detector-element linear-deviation at 2 Mpps (million photons per sec) of 8.9 % (typical) and 12 % (max). When comparing measured and simulated spectra, a low-energy tail is visible in the measured data due to the spectral response of the detector. If no valid photon detections are expected in the low-energy tail, then a background subtraction may be applied to allow for a possible first-order correction. If photons are expected in the low-energy tail, a detailed model must be implemented. A radiograph of an aluminum step wedge with a maximum height of 20 mm shows an underestimation of attenuation by about 10 % at 60 keV. This error is due to partial energy deposition from higher energy (>60 keV) photons into a lower-energy (∼60 keV) bin, reducing the apparent attenuation. A radiograph of a polytetrafluoroethylene (PTFE) cylinder taken using a bremsstrahlung spectrum from an x-ray voltage of 100 kV filtered by 1.3 mm Cu is reconstructed using Abel inversion. As no counts are expected in the low energy tail, a first order background correction is applied to the spectrum. The measured linear attenuation coefficient (LAC) is within 10% of the expected value in the 60 to 100 keV range. Below 60 keV, low counts in the corrected spectrum and partial energy deposition from incident photons of energy greater than 60 keV into energy bins below 60 keV impact the LAC measurements. This report ends with a demonstration of the tomographic capability of the system. The quantitative understanding of the detector developed in this report will enable further study in evaluating the system for characterization of an object’s chemical make-up for industrial and security purposes.

The extensive progress in hardware in recent years makes it now possible to develop nearly real time control system for tomography experiments. Such system can perform all the routines that are necessary for the experiment and provide real time feedback to the user. This feedback can be used for instant monitoring and/or for real time reconstruction. The initial design and implementation of such system was presented in the SPIE publication in 2014 [1]. In this paper an update to the system is presented. The paper will cover the following 4 topics. The first topic simply gives an overview of the system. The second topic presents the way how we integrate different software components to achieve simplicity and flexibility. As it is still in research and design phase we need a possibility to easily adjust the system to our needs introducing new components or removing old ones. The third topic presents a hardware driven tomography experiment design implemented at one of our beamlines. The basic idea is that a hardware signal is sent to the instrument hardware (camera, shutter etc). This signal is emitted by the controller of the sample axis which defines the moment when the system is ready to capture the next image i.e. next rotation angle. Finally as our software is in a constant process of evaluation a continuous integration process was implemented to reduce the time cost of redeployment and configuration of new versions.

The innervation of the inner ear has been thoroughly investigated in humans and in some animal models such as the
guinea pig, the rabbit, the cat, the dog, the rat, the pig and some monkeys. Ruminant inner ears are still poorly known
and their innervation was never investigated despite its potential interest in phylogenetic reconstructions. Following
earlier works on the ontogeny of the cow’s ear, we expand our understanding of this structure by reconstructing the fine
innervation pattern of the inner ear of the cow in two ontogenetic stages, at 7 months gestation and at an adult age. Since
we work on dry skeletal specimens, only the endocast of the innervation inside the petrosal bone was reconstructed up to
the internal acoustic meatus. The paths of the facial and vestibulocochlear nerves could be reconstructed together with
that of the spiral ganglion canal. The nerves have a very fibrous pattern. The bony cavities of the ampular and utricular
branches of the vestibulocochlear nerve could also be reconstructed. Our observations confirm that not all bony
structures are present in foetal stages since the branch of cranial nerve VII is not visible on the foetus but very broad on
the adult stage. The fibrous pattern within the modiolus connecting the spiral canal to the cochlear nerve is also less
dense than in the adult stage. The shape of the branch of cranial nerve VII is very broad in the cow ending in a large
hiatus Fallopii; this, together with the above-mentioned particularities, could constitute relevant observations for
phylogenetical purposes when more data will be made available.

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Journal of Applied Remote SensingJournal of Astronomical Telescopes Instruments and SystemsJournal of Biomedical OpticsJournal of Electronic ImagingJournal of Medical ImagingJournal of Micro/Nanolithography, MEMS, and MOEMSJournal of NanophotonicsJournal of Photonics for EnergyNeurophotonicsOptical EngineeringSPIE Reviews